The ALL-1 gene, the human homologue of the Drosophila trithorax gene, is directly involved in human acute leukemias associated with abnormalities at chromosome 11q23. Using the differential display method, we have isolated genes which are downregulated or upregulated in ALL-1 double knockout mouse embryonal stem (ES) cells including one, designated ARP, which is a novel homeotic gene containing a short motif shared with several homeobox genes. Utilizing a bacterially-synthesized ALL-1 polypeptide encompassing the AT-hook motifs, we identified a 0.5 kb ARP DNA-fragment which preferentially bound to the polypeptide. Within this DNA, a region of -100 bp was protected by the polypeptide from digestion with ExoIII and DNase I. Whole mount in situ hybridization to early mouse embryos of 9.5-10.5 days indicated a complex pattern of ARP expression, spatially overlapping with the expression of ALL-1. These results suggest that ARP is upregulated by the ALL-1 protein, possibly through direct interaction with an upstream DNA sequence of the ARP gene. Expression of ARP is shut off in acute leukemias carrying a t(4;11) or a t(9;11) chromosome translocation suggesting that the 11q23 abnormalities create chimeric products with a dominant negative effect. We intend to identify and characterize gene targets of ALL-1 and to determine their role in hematopoietic differentiation, in embryonal development and in leukemogenesis. Acute lymphoblastic and acute myelogenous leukemias will be investigated for the expression, rearrangements and mutations of ALL-1 target genes.